6n9f: Difference between revisions

<StructureSection load='6n9f' size='340' side='right' caption='[[6n9f]], [[Resolution|resolution]] 3.70&Aring;' scene=''>

<table><tr><td colspan='2'>[[6n9f]] is a 110 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9F FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=KGV:'>KGV</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6n9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9f OCA], [http://pdbe.org/6n9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9f RCSB], [http://www.ebi.ac.uk/pdbsum/6n9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9f ProSAT]</span></td></tr>

[[http://www.uniprot.org/uniprot/RL25_THET2 RL25_THET2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance (By similarity). [[http://www.uniprot.org/uniprot/RL31_THET2 RL31_THET2]] Binds the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RL32_THET8 RL32_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00340] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RL24_THETH RL24_THETH]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345]  Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL27_THET8 RL27_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00539] [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL34_THET8 RL34_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B]  

[[Category: Khabibullina, N F]]

[[Category: Mairhofer, E]]

[[Category: Melnikov, S V]]

[[Category: Micura, R]]

[[Category: Polikanov, Y S]]

[[Category: Reynolds, N M]]

[[Category: Soll, D]]

[[Category: Vargas-Rodriguez, O]]

[[Category: Ribosome structure]]